Structural Characterization of Clostridium acetobutylicum 8-Oxoguanine DNA Glycosylase in Its Apo Form and in Complex with 8-Oxodeoxyguanosine

Abstract

SummaryDNA is subject to a multitude of oxidative damages generated by oxidizing agents from metabolism, from exogenous sources and by ionizing radiation. Guanine is particularly vulnerable to oxidation and the most common oxidative product, 8-oxoguanine (8-oxoG), is the most prevalent lesion observed in DNA molecules. 8-oxoG can form a normal Watson-Crick pair with cytosine (8-oxoG:C), but it can also form a stable Hoogsteen pair with adenine (8-oxoG:A) leading to a G:C →T:A transversion after replication. Fortunately, 8-oxoG is recognized and excised by either of two DNA glycosylases of the base excision repair (BER) pathway, formamidopyrimidine-DNA glycosylase (Fpg) and 8-oxoguanine DNA glycosylase (Ogg). While Clostridium acetobutylicum Ogg DNA glycosylase can specifically recognize and remove 8-oxoG it displays little preference for the base opposite the lesion, which is unusual for a member of the Ogg1 family. This paper describes the crystal structures of CacOgg in its apo-form and in complex with 8-oxo-2'-deoxyguanosine. A structural comparison between the apo and liganded forms of the enzyme reveals a structural reorganization of the C-terminal domain upon binding of 8-oxoG similar to that reported for hOGG1. A structural comparison of CacOgg with hOGG1 in complex with 8-oxoG containing DNA provides a structural rationale for the lack of opposite base specificity displayed by CacOgg.

Structural basis for the lack of opposite base specificity of Clostridium acetobutylicum 8-oxoguanine DNA glycosylase

“…The Ogg DNA glycosylases belong to three different families: Ogg1, which includes the well characterized human OGG1 (hOGG1) and the bacterial Clostridium acetobutylicum Ogg (CacOgg) [11–19], Ogg2 which was the last Ogg family to be structurally characterized and comprises mostly archaeal enzymes [20, 21] and finally, AGOG (Archaeal GO Glycosylase) [22] represented by Pyrobaculum aerophilum AGOG (Pa-AGOG). [23, 24] Overall CacOgg shares a similar tertiary fold with hOGG1.…”

“…Our previously published crystal structure of CacOgg in complex with the nucleoside 8-oxo-2′-deoxyguanosine (8-oxodG) revealed that CacOgg binds the damaged base similarly to hOGG1. However, in contrast to hOGG1 which displays a strong preference for C opposite 8-oxoG with no recognition of 8-oxoG opposite A, CacOgg can cleave the lesion regardless of the opposite base, recognizing 8-oxoG opposite A as well as with C. [11, 19] This relaxed opposite base specificity makes CacOgg quite unusual among the Ogg1 enzymes. Interestingly, two of the four amino acids making interactions with the cytosine in hOGG1 are not conserved in CacOgg, i.e., residues Arg154 and Tyr203 in hOGG1 correspond to Met132 and Phe179 in CacOgg.…”

Crystal Structures of Two Archaeal 8-Oxoguanine DNA Glycosylases Provide Structural Insight into Guanine/8-Oxoguanine Distinction

“…In the crystal structure of hOGG1 Tyr203 interacts with Asn149, which in turn participates in a H-bond with the N4 amine of C. The role of Tyr203 in determining opposite base specificity is indirect and may be to stabilize Asn149. In CacOgg the tyrosine is replaced by a Phe (Phe179); the H-bond with the asparagine residue is lost and Asn127 (which corresponds to hOGG1 Asn149) does not appear to interact with C (Faucher, et al, 2009). In the Ogg2 enzymes the residue corresponding to hOGG1 Ty203 is also a phenylalanine (Phe85 in MjaOgg and Phe81 in SsoOgg).…”

Probing the activity of NTHL1 orthologs by targeting conserved amino acid residues

“…The unliganded EcoNth structure [22] superimposes well on the GstNth structure, so it is an appropriate model to use to identify residues at or near the active site. No structure for hNTHL1 is available, but because of the similarity between other human and bacterial HhH-GPD proteins (for example hOGG1 and CacOgg [23], it was assumed that hNTHL1 has a similar active site as GstNth and EcoNth. A method of bioinformatics sequence analysis also guided selection of residues with possible importance to specificity, based on work by Gu [24].…”